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Allozyme variation was examined in seven species and four varieties of Caulerpa sampled from the Great Barrier Reef (GBR) region, Australia. Differences between species were greater than those between populations of the same taxon sampled from different geographical locations, and typically included fixed gene differences (no alleles found in one taxon shared by the other taxon) at two or more loci. Three varieties of C. racemosa, vars imbricata, laetevirens, and racemosa, and a peltate morph of C. racemosa were as strongly distinguished genetically as the six other species examined: C. cupressoides, C. lentillifera, C. peltata, C. serrulata, C. sertularioides, and C. taxifolia. Cluster analysis did not place all of the C. racemosa varieties together and linked them with other species, but cladistic analyses showed the allozyme data gave little useful phylogenetic information. Eight of 13 plants identified initially as C. serrulata were distinguished at several loci, indicating the presence of an undetermined cryptic taxon. Population genetic analysis of polymorphisms, which occurred in some taxa, demonstrated strong spatial differentiation among populations of C. cupressoides, C. racemosa vars laetevirens and racemosa, C. serrulata, and C. taxifolia and significant but variable degrees of clonality and/or inbreeding within these populations. Allozymes proved to be a useful tool for defining species boundaries and investigating population structure in Caulerpa, but not for determining phylogenetic relationships within the genus. [ABSTRACT FROM AUTHOR]